Australian Centre for Plant Functional Genomics (ACPFG)

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Browsing Australian Centre for Plant Functional Genomics (ACPFG) by Author "Bader, D.A."

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    Computing a consensus of multilabeled trees
    (Society for Industrial and Applied Mathematics, 2012) Huber, K.; Moulton, V.; Spillner, A.; Suchecki, R.; 14th Meeting on Algorithm Engineering and Experiments 2012 (ALENEX12) (16 Jan 2012 - 16 Jan 2012 : Kyoto, Japan); Bader, D.A.; Mutzel, P.
    In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have occurred in the past. We present exact algorithms for solving (1) and (2) that have an exponential runtime in the worst case. To give some impression of their performance in practice, we apply them to simulated input and to a real biological data set highlighting the impact of several structural properties of the input on the performance. Copyright © SIAM.